At first, an aspect of this episode galled me. The Doctor asks Clara ‘am I a good man?’ seemingly out of the blue. Why doesn’t he know he’s a good man? He saved Gallifrey, he defended Trenzalore, he’s just saved a soldier from certain death. It seems like angst for angst’s sake, a way to bookend the episode, with Rusty’s ‘you are a good Dalek’ forming the other bookend.
There are theories floating about that the Doctor was discombobulated from his recent regeneration and can no longer be sure if he’s a good person or not. I don’t think that’s true.
It’s not the regeneration that’s upset the Doctor at all. Neither his question nor Clara’s eventual answer - ‘you try to be’ - even give any indication that anything important has changed between them. Indeed, ‘you try to be’ suggests an ongoing familiarity, an implication that things have always been this way, not a recent innovation.
No, what’s bothered the Doctor is the prospect of being injected into a Dalek. His immediate reaction is ‘You can’t put me in there!’ He doesn’t dare to enter that moral event horizon on his own, without a touchstone. He knows (back from the days when he looked like Chris Ecclestone, if nothing else) that where the Daleks are concerned, his own morals are decidedly grey. There’s no solid bottom of certainty there. He cannot trust himself.
And that’s why he asks Clara what he does, in the way that he does. He is NOT seeking reassurance. The last thing he wants is to be patted on the arm and told he’s a good man and not to worry about it. He asks her because he knows that if she is truly as honest as he needs her to be, she won’t be able to give him a definitive answer. Which is why, after she is unflinchingly honest with him, he says ‘I need you.’ She’s proven that he can still trust her to tell him the truth. It’s a test, and she passes it.
He needs her to act as his moral barometer, because they are going ‘into darkness’. That’s the point. He doesn’t need a single pat answer that would reassure him that he’s intrinsically good, he needs a frank and honest companion. Because it’s dark where they’re going, and there be monsters.
My mistake was to take the Doctor’s apparent arbitrary doubts at face value. He simply needed to know if he could trust Clara’s honest moral judgement before he dared to go (dun dun dunnn) into the Dalek.
(The Doctor says he’s terrified of what Clara’s answer might be before he asks if he’s a good man. But what answer was he terrified he might hear? The immediate reaction is to think that he’s terrified of hearing a ‘no’. But on reflection, there’s no grounds for being scared of that; if Clara honestly thought he was a bad man, why would she still be associating with him? I think he was terrified that she’d say ‘yes’ out of a wish to reassure him, and not because she honestly believed it. Which would have been fatal, because her honesty is what he needs most to light his way in the ‘darkness’ of the Dalek.)